fbpx Strategic Salmon Health Initiative | Pacific Salmon Foundation


Kristi Miller Saunders

Kristi Miller-Saunders, with Fisheries and Oceans Canada Pacific Biological Station, is leading genomic research for the initiative.
Photo by Nik West


Strategic Salmon Health Initiative


In the Pacific Northwest, Chinook, sockeye, coho salmon and steelhead trout have experienced precipitous declines over the past 30 years, with many populations threatened or endangered, and some already extinct. Our program applies a series of novel molecular and ecological approaches to understand the role of infection and disease outbreaks in salmon declines, a difficult task when mortality is mostly unobservable. High throughput pathogen monitoring tools have revealed the distribution and abundance of over 60 potential salmon pathogens (viruses, bacteria, fungal and protozoan parasites) in 28,000 wild, hatchery and cultured salmon.


Since 2013, the Pacific Salmon Foundation has embarked on a remarkable partnership with Genome BC and Fisheries and Oceans Canada.  This partnership, called the Strategic Salmon Health Initiative, was started for a variety of reasons, the primary one being the high mortality rate of juvenile salmon during their early ocean migration. There is a strong belief within the scientific community that infectious disease may be a significant factor in this mortality, but not enough is known about what disease agents might affect Pacific salmon in their natural habitats. What is known comes almost exclusively from observations of cultured fish (both in hatcheries and aquaculture). The initiative intends to clarify the presence and/or absence of microbes in Pacific salmon. 


PSF pens letters to P.M. and B.C. Premier reagaring Sea Lice and Discovery Islands

In August, PSF wrote letters to the Prime Minister and B.C. Premier regarding alarming unnatural sea lice loads on out-migrating Pacific salmon in Discovery Islands. The letters reiterate the PSF position that in the absence of strong proof otherwise, and given the current state of many salmon populations in southern BC, government should immediately and significantly reduce the number of open-net pen salmon farms in the Discovery Islands and Johnstone Strait. The letters also outline a five-point plan to encourage a transition to closed containment salmon farming in British Columbia. PSF wrote the letters to add support for the concerns and objectives expressed in a recent open letter from a co-operative group of commercial and recreational fishing organizations, religious organizations, marine tourism operators, environmental groups, and First Nations.

Letter to Prime Minister

Letter to Premier of B.C


Click Here to access new findings from the Strategic Salmon Health Initiative (SSHI) related to Piscine orthoreovirus (PRV) in British Columbia. 


View the full publication list for the Strategic Salmon Health Initiative here: Click Here 


Learn more about the project and Genome BC: http://www.genomebc.ca/index.php?cID=1235

Read the press release 

Read the backgrounder 


Additional Information

Models informed by a decade of infection data in juvenile Chinook salmon sampled during early marine residence has revealed that temperature is the most significant driver of infection, with exposure to aquaculture, proximity to freshwater, age at ocean entry, hatchery or wild origin, stock, and latitude associated with a more limited number of pathogens.

Models are also beginning to resolve the pathogens most closely correlated with year-class strength, some transmitted in freshwater, and others in the early marine environment. Climate warming is a major factor for salmon to contend with. Impacts can directly cause stress in salmon, but also indirectly impact prey availability and predator distributions, as well as disrupting the natural balance between pathogens and their hosts.

New research from the SSHI  was published September 3 in the online journal eLife . Three newly discovered viruses—including one from a group of viruses never before shown to infect fish—have been found in endangered Chinook and Sockeye salmon populations. The impact of these viruses on salmon health isn’t yet known, but we do know that two of the viruses impact the same tissues in salmon as other species, and cause serious diseases in those species. Of note, two of the three viruses were found in wild salmon, one was observed in hatchery facilities and all three were associated with Chinook aquaculture. The  paper raises questions about whether these viruses are contributing to declines in wild Chinook and sockeye stocks. Further research is required to understand the full implications of these findings.

Prior to these findings, an outbreak of Heart and Skeletal Muscle Inflamation (or HSMI) was found via the SSHI in fish from one farm. The lesions in the fish are the same as those previously identified by the same histopathologist in farm audit samples collected from  farms during 2011-2013. The HSMI finding was formally reported to the industry and Fisheries and Oceans Canada as per the scientific protocol for the project and announced by Fisheries and Oceans Canada <click here for the release>. As HSMI is not an OIE reportable disease, it was not reported to the Canadian Food Inspection Agency. A slide presentation on the HSMI finding can be viewed here.

Dr. Kristi Miller (Saunders) is an aquatic molecular biologist with expertise in genetics, genomics, transcriptomics, immunogenetics, and fish health, with research on Pacific and Atlantic salmon spanning 27 years. Fisheries and Oceans Canada; University of British Columbia (adjunct).